In a frugal installation of Puppy the linux directory structure is contained in a read-only SFS file (also known as PupSfs) . It contains the original configuration of the Puppy version and RootFS; any changes are stored in a SaveFile.

For example, the BaseSFS file in Puppy 5.28 is lupu_528.sfs.

Only files stored in the /mnt directory will be saved outside the SaveFile. For example, /mnt/home and /mnt/sda2 are the root directories of the boot partition and sda2 partition respectively.